diff --git a/doc/doxygen.warnings.report.sh b/doc/doxygen.warnings.report.sh
index 4ca193112..b126ca372 100755
--- a/doc/doxygen.warnings.report.sh
+++ b/doc/doxygen.warnings.report.sh
@@ -301,7 +301,7 @@ else
     # Modify doxygen.conf to generate all the warnings
     # (We also suppress dot graphs, so shorten the run time.)
 
-    conf=doxygen.conf
+    conf=doc/doxygen.conf
     cp $conf ${conf}.bak
     cat <<-EOF >> $conf
     
@@ -333,7 +333,7 @@ EOF
     fi
 
     # Waf insists on writing cruft to stdout
-    sed -i -E '/^Waf:/d' $intro_h
+    sed -i -E '/^Waf:/d' doc/$intro_h
 
     verbose -n "Rebuilding doxygen docs with full errors"
     (cd "$ROOT" && ./waf --doxygen-no-build >&6 2>&6 )
diff --git a/src/core/model/command-line.cc b/src/core/model/command-line.cc
index be37f8cd4..d5275188d 100644
--- a/src/core/model/command-line.cc
+++ b/src/core/model/command-line.cc
@@ -339,11 +339,6 @@ CommandLine::PrintDoxygenUsage (void) const
 {
   NS_LOG_FUNCTION (this);
 
-  {
-    char buf[1024];
-    std::string cwd= getcwd (buf, 1024);
-  }
-  
   const char * envVar = std::getenv ("NS_COMMANDLINE_INTROSPECTION");
   if (envVar == 0 || std::strlen (envVar) == 0)
     {
diff --git a/src/core/model/command-line.h b/src/core/model/command-line.h
index 70e3b966b..ad195918c 100644
--- a/src/core/model/command-line.h
+++ b/src/core/model/command-line.h
@@ -230,6 +230,8 @@ public:
    *
    * This form is required to generate Doxygen documentation of the
    * arguments and options.
+   *
+   * \param [in] filename The source file name.
    */
   CommandLine (const std::string filename);
   /**